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Willow, Anya, and Xander are playing three-handed poker since Buffy is elsewhere. Xander tells his plan to sell supposedly healthy (but nasty tasting) Boost bars. They question the intentions of The Initiative. In a field test against the commandos, Buffy impresses Professor Walsh. The next day in the cafeteria, Buffy gushes about her performance to Willow. Willow confirms that The Scooby Gang, including Buffy, will assemble at The Bronze that night. Willow obviously misses Buffy, who has been rather busy of late.

Giles visits Spike at his new crypt to pay the money he owes from the previous episode in which Spike charged him for his help. Spike makes it clear that he will not help them again and wants nothing to do with the Scoobies. Riley takes Buffy into the Initiative. Professor Walsh gives her a tour of the impressive facility. Buffy is made a member of the team. However, a slip from Buffy indicating her prior knowledge of the Initiative's behavior modification research (viz. Spike's chip) does not go unnoticed. Tara tries to give a crystal to Willow, a family heirloom, but Willow refuses to accept the powerful magical implement. Tara invites Willow to try some spells with the crystal that night. Willow reluctantly declines due to her plans with the Scoobies. Professor Walsh enters Room 314 in the secure lab area to check up on her special project: a part-demon, part-human, part robot creature named Adam.

Buffy is an hour late meeting her friends at the Bronze, and when she does show, she brings Riley and the team. Buffy reveals that she is now working with the Initiative. Willow questions how much trust Buffy should put in the organization. Suddenly Buffy rushes off with the team. Abandoned by Buffy, Willow goes to Tara's dorm room after all. Buffy and the commandos deploy in two teams in search of a Polgara demon. They are instructed to keep the demon's arms, which contain vicious spears, intact.

Forrest spots Hostile 17 (Spike) and sends his team after the vampire. Spike gets away, but they shoot him with a tracer to be able to track him later. The Polgara demon attacks the Alpha team; Buffy and Riley, fighting together, apparently kill it. Stimulated, they have sex (for the first time) in Riley's dorm room. Professor Walsh watches them from a secret camera. Waking up in the morning, Buffy is a little surprised to see that Riley is still in bed by her side. Riley takes a number of pills ("my vitamins," he says). They talk, but when Buffy asks about "314", Riley immediately receives a call from Professor Walsh with an assignment. Walsh and Dr. Angleman decide that it is time to go with their plan to get rid of Buffy.

Desperate and unable to shake off the commandos, Spike goes to Giles for help. Giles tries to remove the tracer from Spike's shoulder, but it's in deep. Riley reinforces Forrest's team. With the soldiers gone, Walsh summons Buffy for a very easy mission and arms her with a stun rifle. Wearing a heart monitor and sound camera, Buffy goes out alone. The mission is a trap. The rifle shorts out, the exit is barred, and Buffy is set upon by two powerful demons armed with axes.

With Willow doing a masking spell to buy time and Spike babbling from drink in lieu of anesthesia, Giles finally manages to remove the tracer from the vampire's shoulder. They flush it down the toilet just in time to misdirect Riley and his team. Buffy kills the demons, but in the fight the monitor falls off. With no reported heartbeat or movement Walsh assumes that she is dead. When Riley returns, she informs him that Buffy is dead and adds a few more lies. In the middle of her "eulogy" Buffy picks up the camera and reveals, in full view of Riley, Walsh's trap. Riley walks out on Walsh.

The Initiative has grafted an arm from the Polgara demon to Adam. Walsh, upset that she had to sacrifice Buffy and Riley's loyalty to safeguard her great project (Adam), goes to Room 314 and speaks as if to the sleeping creature. Adam wakes and skewers Walsh with his new arm spear, saying "Mommy." She falls over dead.

One of the overarching themes of Season Four, Buffy's friends feeling alienated from her role as the Slayer, is portrayed when Willow feels left out and hesitant about Buffy joining the Initiative. In "A New Man" it was Giles who felt left out of Buffy's life and duties. This theme culminates in the episode "Primeval".

The fact that Riley is still with Buffy in the morning is a marker of his morally unambiguous intentions, unlike the soulless Angelus or the libertine Parker.

Learning that Professor Walsh is up to no good, Riley walks out on the Initiative. After she is dead he returns to help because of his loyalty to his teammates and his belief in the mission of the Initiative.

Adam will become the Big Bad of the season, taking over from Professor Walsh.

Willow and Tara's relationship starts to take a romantic turn although no romantic affection is explicitly shown. The network was very reluctant to allow an explicit lesbian relationship.[1]

Willow and Tara's relationship is foreshadowed a couple of times in this episode. First, when Willow prays for the heart she needs in the poker game. Next, when Willow notes "everybody's getting spanked but me", alluding to the fact that she is the only one without a bed buddy.